Genome wide identification of genic and non-genic Microsatellites in Nilaparvata lugens Stål

Abstract

The brown plant hopper (BPH), Nilaparvata lugens Stal (Homopterous: Delphacidae) is one of the lethal pests in rice. In the present study, genome wide distributed Simple Sequence Repeats (SSR) were identified and analysed. The screening of 1.2 Gb of BPH genome resulted in identification of 271785 SSRs. Out of these, 3231 SSRs were from genic region. Microsatellite distribution in genome was found to be 238.2 SSRs per Mb. Altogether the microsatellite motifs contribute only 7.45Mb of BPH genome. Trinucleotide repeats were most abundant representing 50.8% of total genomic microsatellites. Longer repeat motifs were found to be least abundant in the genome representing 1.1% and 0.5% for pentanucleotide and hexanucleotide, respectively. SSR markers identified from this study can be useful for diversity analysis and genetic map development of BPH.